Academic workflows revisited

It’s been a year since I wrote this post on academic workflows. The way I work has changed a bit since then – some apps have gone out, some have been added, and the relationship between some of them have changed, primarily affecting my literature review work flow. Here’s a little post on my current set up.

The data analysis process

This is pretty identical to what I wrote in my previous post. I still think Inqscribe is great for transcription, Curio (which I’ve written about here) is great for overall management of the writing process, and iAnnotate is great for those first rounds of analysis of my overall data corpus. In addition to Curio, I often turn to NovaMind, which is a mind mapping app with an extensive feature set.

The writing process

I also handle the writing process pretty much the same way as I outlined a year ago.

I use mind mapping and outlining tools for brainstorming and organising my ideas (which I’ve written about here and here). I use Scrivener for my writing (which I’ve written about here), and import literature notes, data and pdfs as needed. Scrivener is a fantastic tool for writing academic papers, and I can’t see myself giving up on it anytime soon. When their long awaited iPad app arrives, it will be even more useful.

Towards the end of the writing process, I switch to Word. I use Endnote for citations, inserting unformatted citations in Scrivener and then converting them when the text is in Word.

The literature review process

Here’s where most of the changes have happened. I no longer use Sente. I still think it’s a very decent app, but eventually I decided to go with Bookends (which I’ve written more about here). There were two main reasons for this. The first is the ability to do a spotlight search of imported attachments and subsequently create a smart group based on the search results. I find this very useful for review purposes, and it’s a feature that Sente doesn’t have. The second reason is the extremely responsive support – the developers get back to you very quickly, and they stay with you until the problem is solved.

So, what I typically do with my literature is as follows:

Importing literature. I subscribe to email notifications from all the journals in my academic field. From the email, I open the table of contents in Safari, and from there I import the pdfs I want into Bookends using the print feature. I then use keywords (Bookends’ name for tags) to assign each article to the relevant thematic smart group(s). I use Hazel to automatically add a copy of the downloaded pdf to a dropbox folder. This is because I want to keep a ‘clean’ copy in addition to the pdfs that I annotate.

Reading and marking up journal articles. I then turn to my iPad. I prefer reading and marking up literature on my iPad, rather than on my Air. I can hold it in the same way as a book, and use a stylus to highlight, underline and write notes. The attachments folder in Bookends is synced to Dropbox, which in turn is synced to GoodReader and iAnnotate (which I’ve written about here) on my iPad. I use GoodReader and iAnnotate to mark up journal articles. When I’m done, I extract the annotations from the pdf file, and send them to myself in an email. My email client Postbox comes with good Evernote integration, which allows me to easily convert the email to a note in Evernote. You can also simply cut and paste the text, or use Skim as described by Joseph Flanagan in the comments below.

Note taking. I have two main hubs for literature notes: Evernote (which I’ve written about here) and Circus Ponies Notebooks (which I’ve written about here).

In Evernote, I put all ‘single source notes’ – those are notes from a particular journal article, book chapter or book. Each source has a separate note, which includes the formatted reference, the abstract, annotations made on my iPad, and my own reflections about the text and its relevance for my work. These notes are gathered in a separate notebook called ‘review’, and organised according to tags that reflect the smart groups I have created in Bookends. Some of the reasons why I use Evernote as a hub for my single source notes, is that it works cross platform – the sync between my Air, iPad, android phone and Windows machine at the office is instant. I also like the ease with which I can organise and share my notes, and that I can create link between notes. Once the notes have been written up, I return to Bookends and use labels to mark the relevant reference with “in EN”, to make it visible that this reference has a set of notes and annotations in Evernote.

I use CPN for reviews that are organised according to theme, rather than author/single text. I find it superior to Evernote for this purpose, due to the outlining feature of the notes pages. Outlining makes it easy to create different hierarchical levels for different kinds of information (theme, author, findings, and so on). It’s also convenient for navigating long documents, because you can expand and collapse information as needed. I also create links between different cells and pages, so I can easily refer back to things I’ve already written and connect related content.

I export notes from both of these apps into Scrivener when I need them during writing.

…so – that’s more or less my current set up. If you have suggestions for good academic work flows, please leave a comment below.